SMTL ID : 5ds7.1

2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 18 residues within 4Å: Chain A: G.35, Y.36, T.37, I.67, A.68, A.69 Chain C: I.15, G.44, K.45, G.46, S.47, H.48, Y.51, L.63, S.90, G.91, V.92, F.94 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:Y.36, A:A.69, A:A.69, C:S.47, C:S.47, C:S.47, C:H.48, C:G.91 Salt bridges: C:H.48 pi-Stacking: C:F.94 AMP.2: 19 residues within 4Å: Chain A: G.44, K.45, G.46, S.47, H.48, Y.51, L.63, S.90, G.91, V.92, F.94 Chain B: G.35, Y.36, T.37, I.67, A.68, A.69, K.105, F.106 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.47, A:S.47, A:H.48, A:G.91, B:G.35, B:T.37, B:A.69, B:A.69 Water bridges: A:H.89, B:K.34, B:K.105 pi-Stacking: A:F.94 Salt bridges: B:K.105 AMP.4: 20 residues within 4Å: Chain B: I.15, G.44, K.45, G.46, S.47, H.48, Y.51, L.63, S.90, G.91, V.92, F.94 Chain C: G.35, Y.36, T.37, I.67, A.68, A.69, K.105, F.106 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:T.37, C:A.69, C:A.69, B:S.47, B:S.47, B:S.47, B:H.48, B:G.91 Water bridges: C:K.34 Salt bridges: C:K.105, B:H.48

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: V.92, V.93 Chain B: R.102, F.106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wheatley, N.M. et al., A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. J.Mol.Biol. (2016)

Release Date

2016-09-28

Peptides

Nitrogen regulatory protein P-II: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Nitrogen regulatory protein P-II

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